Detection and identification of mycobacteria

Abstract: Genus- and species-specific oligonucleotide probes derived from the M. paratuberculosis 70kD heat shock protein gene sequence. The probes are useful for detecting Mycobacteria and for identifying specific species of Mycobacteria.

Description: FIELD OF THE INVENTION The Mycobacteria are a genus of bacteria which are acid-fast, non-motile, gram-positive rods. The genus comprises several species which include, but are not limited to, Mycobacterium africanum, M. avium, M. bovis, M. bovis-BCG, M. chelonae, M. fortuitum, M. gordonae, M. intracellulare, M. kansasii, M. microti, M. scrofulaceum, M. paratuberculosis and M. tuberculosis . Certain of these organisms are the causative agents of disease. For the first time since 1953, cases of mycobacterial infections are increasing in the United States. Of particular concern is tuberculosis, the etiological agent of which is M. tuberculosis . Many of these new cases are related to the AIDS epidemic, which provides an immune compromised population which is particularly susceptible to infection by Mycobacteria. Other mycobacterial infections are also increasing as a result of the increase in available immune compromised patients. Mycobacterium avium, Mycobacterium kansasii and other non-tuberculosis mycobacteria are found as opportunistic pathogens in HIV infected and other immune compromised patients. At the present time the diagnosis of mycobacterial infections is dependent on acid-fast staining and cultivation of the organism, followed by biochemical assays. These procedures are time-consuming, and a typical diagnosis using conventional culture methods can take as long as six weeks. Automated culturing systems such as the BACTEC™ system (Becton Dickinson Microbiology Systems, Sparks, MD) can decrease the time for diagnosis to one to two weeks. However, there is still a need to reduce the time required for diagnosing Mycobacterial infections to less than a week, preferably to about one day. Oligonucleotide probe based assays such as Southern hybridizations or dot blots are capable of returning a rapid result (i.e., in one day or less) but for diagnosis of Mycobacterial infections such methods would require an oligonucleotide probe which is specific for the genus of Mycobacteria or specific for a particular mycobacterial species if specific identification of the organism is desired. Probes of the required specificity have not previously been available for the gene encoding the 70K heat shock protein. Heat shock proteins are a family of proteins which are expressed in elevated amounts when an organism is challenged by an increase in temperature. The heat shock proteins are highly conserved (R. J. Garcia, et al. (1989) Infection and Immunity 57 :204-212; R. S. Gupta, et al. (1992) J. Bacteriology 174 :4594-4605). One such heat shock protein which is highly conserved in all living cells is approximately 70kD in size and is referred to as hsp 70. The 70kD heat shock protein has been identified in M. tuberculosis (R. B. Lathigra, et al. (1988) Nucleic Acids Res. 16 :1636), M. leprae (K. R. McKenzie, et al. (1991) J. Immunol. 147 :312-319) and M. paratuberculosis (K. Stevenson, et al. (1991) Nucleic Acids Res. 19 :4552). Stevenson, et al. report a stretch of 133 amino acids (amino acids 407-540) in the M. paratuberculosis 70kD heat shock protein which is 90% homologous to amino acids 131-264 of the M. leprae 70kD heat shock protein and to amino acids 3-134 of the M. tuberculosis 71 kD heat shock protein. One embodiment of the present invention provides oligonucleotide probes which are specific for the genus Mycobacteria and do not exhibit any cross-reactivity with closely related microorganisms such as Rhodococcus rhodochrous and Nocardia asteroides . In a second embodiment, oligonucleotide probes are provided which are specific for selected species of Mycobacteria , R. rhodochrous or N. asteroides. These probes may be used after culturing as a culture confirmation tool. Alternatively, the probes may be used prior to culturing in detection and identification methods in which the bacterial DNA is amplified. In either case, the inventive probes and diagnostic methods provide a means for rapidly discriminating between Mycobacteria-positive and Mycobacteria-negative samples, allowing the practitioner to rapidly identify a sample as negative or positive for Mycobacteria and thereby avoid the time consuming task of culturing negative samples. Species-specific probes allow rapid identification of the specific etiological agent involved in a mycobacterial infection and provide information which can be used in determining appropriate therapy in a short period of time. SUMMARY OF THE INVENTION The present invention provides Mycobacteria genus- and species-specific oligonucleotide probes derived from the gene encoding the M. paratuberculosis 70kD heat shock protein. A 349 bp portion of the hsp70 gene was identified in eleven Mycobacteria species by polymerase chain reaction (PCR) amplification using defined primers. The amplification products were subcloned, sequenced and aligned. Similar sequence information was obtained from R. rhodochrous and N. asteroides and these sequences were also aligned to obtain probes which would not cross-react with R. rhodochrous or N. asteroides . A 204 bp segment corresponding to upstream sequences of the M. paratuberculosis hsp70 gene were identified in M. avium, M. gordonae, M. tuberculosis, N. asteroides and R. rhodochrous and also used to design genus-specific probes. DETAILED DESCRIPTION OF THE INVENTION The oligonucleotide probes of the present invention are derived from a 349 bp segment and a 204 bp segment of the M. paratuberculosis hsp70 gene and are useful for rapid detection of Mycobacteria by nucleic acid hybridization. The probes may either be hybridized directly to mycobacterial DNA and detected, or they may be used as primers in nucleic acid amplification reactions to produce Mycobacteria-specific amplification products which may then be detected. The probes may be of any length suitable for the particular assay format employed. In general, they are at least about 10-15 nucleotides in length. For detecting Mycobacteria they are preferably about 15-20 nucleotides in length. When used as primers in nucleic acid amplification reactions for amplification of Mycobacteria-specific target DNA, the target DNA is preferably 50-150 nucleotides in length. The probes may be either deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) and may have either a naturally-occurring sugar-phosphate backbone or a backbone modified to include phosphorothioates, dithionates, alkyl phosphonates or α-nucleotides as is known in the art. The probes may be produced by chemical synthesis of the oligonucleotides, by cloning and amplification in a host cell, or by other means known in the art. Probes according to the invention are hybridized to nucleic acid-containing samples suspected of containing Mycobacteria. The samples may comprise isolated nucleic acids or may be clinical samples. Typically, clinical samples are in the form of a biological fluid or tissue, e.g., sputum, bronchial washings, gastric washings, blood, milk, lymph, skin and soft tissues. As Mycobacteria infect both human and non-human animal species, the present invention is applicable to both human and veterinary diagnostic procedures and the sample may be obtained from either source. For example, M. paratuberculosis is the causative agent of Johne's disease in cattle and has been implicated in Crohn's disease in humans. M. bovis causes tuberculosis in cattle and is transmissible to humans. The present probes and methods may therefore be used to diagnose infection in cattle and to test cattle milk for the presence of M. bovis which may be transmitted to humans. Similarly, M. avium and M. intracellulare infect birds and swine, respectively, and the instant probes and methods may be used to detect such infections. In addition, humans are susceptible to infection form a variety of Mycobacteria, including M. tuberculosis , M. kansasii, M. avium, M. intracellulare, M. scrofulaceum and M. fortuitum and the instant probes and methods may be used to identify the particular species involved as an aid in determining appropriate therapy. The oligonucleotide probes are used to detect and/or identify Mycobacteria by hybridization to mycobacterial nucleic acid. In one embodiment, the probes are used in hybridization methods for direct detection of target mycobacterial nucleic acid. These methods include Southern blots for detection of DNA, Northern blots for detection of RNA and dot blots for detection of either DNA or RNA. These methods are generally well-known in the art and are described in Molecular Cloning: A Laboratory Manual , 2nd ed., J. Sambrook, E. F. Fritsch and T. Maniatis, Cold Spring Harbor Laboratory Press, 1989. In a second embodiment, the presence of mycobacterial nucleic acid in a sample is detected and/or identified by genus- or species-specific amplification of target nucleic acid sequences. In this embodiment, the probes of the invention are used as primers in conventional nucleic acid amplification protocols. Any amplification protocol which relies on hybridization of primers to the target nucleic acid may be used, e.g., PCR (U.S. Patent Nos. 4,683,195; 4,683,202; 4,800,159; 4,965,188), ligase chain reaction (LCR) (R. Weiss (1991) Science 254 :1292), strand displacement amplification (SDA) (G. Walker, et al. (1992) PNAS 89 :392-396; G. Walker, et al. (1992) Nucleic Acids Res. 20 :1691-1696), nucleic acid based sequence amplification (NASBA) (U.S. Patent No. 5,130,238 to Cangene), transcription based amplification (D. Kwoh, et al. (1989) PNAS 86 :1173-1177), self-sustained sequence replication (J. Guatelli, et al. (1990) PNAS 87 :1874-1878) or the Qβ replicase System (P. Lizardi, et al. (1988) Bio Technology 6 :1197-1202). When SDA is employed, the oligonucleotide probes are preferably selected such that the GC content is low, preferably less than 70% of the total nucleotide composition of the probe. Similarly, for SDA the target sequence preferably has a low GC content to minimize secondary structure. As nucleic acids do not require complete complementarity in order to hybridize, it is to be understood that the probe sequences herein disclosed may be modified to some extent without loss of utility as Mycobacteria genus- and species-specific probes. As is known in the art, hybridization of complementary and partially complementary nucleic acid sequences can be obtained by adjustment of the hybridization conditions to increase or decrease stringency (i.e., adjustment of hybridization temperature or salt content of the buffer). In general, sequences at least 65% homologous to the probe sequences disclosed can be used in hybridizations as Mycobacteria genus- and/or species-specific probes without significant loss of specificity. The nucleic acid product of amplification using the inventive probes may be detected by a characteristic size e.g. , on polyacrylamide or agarose gels stained with ethidium bromide. Alternatively, mycobacterial nucleic acid in a sample or specifically amplified mycobacterial nucleic acid may be detected by hybridization to the inventive probes. For detection by hybridization the oligonucleotide probes are typically tagged with a detectable label. The detectable label is a moiety which can be detected either directly or indirectly as an indication of hybridization of the probe to the target nucleic acid. For direct detection of the label, probes may be tagged with a radioisotope and detected by autoradiography or tagged with a fluorescent moiety and detected by fluorescence as is known in the art. Alternatively, the probes may be indirectly detected by tagging with a label which requires further addition of reagents to render it detectable. Indirectly detectable labels include, for example, chemiluminescent agents, enzymes which produce visible reaction products and ligands (haptens, antibodies or antigens) which may be detected by binding to labeled specific binding partners. Particularly useful labels include biotin (detectable by binding to labeled avidin or streptavidin) and enzymes such as horseradish peroxidase or alkaline phosphatase (detectable by addition of enzyme substrates to produce colored reaction products). Methods for adding such labels to, or including such labels in, oligonucleotides are well known in the art and any of these methods are suitable for use in the present invention. For amplification reactions, the tagged detector probes may be the probes used as primers as these are incorporated into the amplification product, or at least one tagged probe different from the primers, which would be expected to hybridize to the amplification product, may be used. For convenience, probes for genus-specific or species-specific detection of Mycobacteria may be packaged in the form of a kit which may further include other components and reagents for performing the detection methods. By way of example, such a kit contains at least one probe according to the present invention, a hybridization solution such as 6X SSC (0.9M sodium chloride, 0.09M sodium citrate, pH 7.0), 0.1M EDTA pH 8.0, 5X Denhardt's solution (0.1% w/v FICOLL TYPE 400, 0.1% w/v polyvinylpyrrolidone, 0.1% w/v bovine serum albummin) and 100 µg/ml sheared denatured salmon sperm DNA. This hybridization buffer is commercially available from Bethesda Research Laboratories. Gaithersburg, MD. See also Molecular Cloning: A Laboratory Manual , supra. The components of the kit are packaged together in a common container, typically including instructions for performing a specific embodiment of the inventive methods. Additional, optional components may also be included in the kit, e.g., a second probe suitable for use with the first probe for amplification of target nucleic acid (or two pairs of probes for LCR), one or more detection probes tagged with a label, and reagents or means for performing detection of the label. The following experimental examples are given as illustration of certain embodiments of the invention. They are not to be construed in any way as limiting the invention as defined by the appended claims. EXAMPLES STRAINS AND DNA PREPARATION The Mycobacteria strains used were as follows: M. africanum LCDC501, M. avium ATCC25291, M. bovis CDC4, M. bovis-BCG CDC34, M. chelonae TMC1543, M. fortuitum TMC1529, M. gordonae TMC1318, M. intracellulare ATCC13950, M. kansasii TMC1201, M. microti LCDC203, M. scrofulaceum CDC78, M. tuberculosis ATCC27294. Non-mycobacterial microorganisms used were as follows: Bordetella pertussis ATCC8467, Candida albicans ATCC44808, Corynebacterium diphtheriae ATCC11913, Escherichia coli ATCC11775, Flavobacterium meningisepticum ATCC13253, Nocardia asteroides ATCC3308, Rhodococcus rhodochrous ATCC13808, Streptococcus pneumoniae ATCC6303, Acinetobacter lwoffi ATCC19001, Enterobacter aerogenes ATCC13048, Enterobacter cloacae ATCC13047, Haemophilus influenzae Type B ATCC33533, Klebsiella pneumoniae ATCC13883, Listeria monocytogenes ATCC7644, Moraxella osloensis ATCC9281, Morganella morganii ATCC25830, Neisseria lactamica ATCC23970, Neisseria meningitidis ATCC13077, Oerskovia turbata ATCC33225, Proteus vulgaris ATCC13315, Pseudomonas aeruginosa ATCC27853, Serratia marcescens ATCC8100, Shigella dysenteriae ATCC13313, Staphylococcus aureus ATCC25923, Staphylococcus epidermidis ATCCE155, Streptococcus pyogenes ATCC19615, Adenovirus Sigma D3390, Eukaryotic DNA From McCoy cells. The Mycobacteria strains were cultured in BACTEC vials in Middlebrook 7H9 media, then heat killed at 70°C for 4 hours. Genomic DNA was isolated as described by S. Visuvanathan, et al. ((1989) J. Microbiol. Mtds. 10 :59-64. Non-mycobacterial strains were cultured in Luria broth or other suitable media, e.g., streptococci in Todd Hewitt broth, Neisseria and Hemophilus on chocolate II agar plates and Nocardia and Rhodococcus in Actinomyces broth. Genomic DNA was isolated by the CTAB mini-prep method of F. M. Ausubel, et al. ((1987) Current Protocols in Molecular Biology , Greene Publishing Associates and Wiley-Interscience, NY). NUCLEIC ACID AMPLIFICATION AND CLONING Stevens, et al. reported a 133 amino acid sequence in the Mycobacterium paratuberculosis 70 kd heat shock protein which is 90% homologous among M. paratuberculosis, M. tuberculosis and M. leprae. This stretch of amino acids is encoded by nucleotides 1415-1814 of the gene sequence. GENBANK69 was searched with the nt 1415-1814 sequence and it showed 87% homology to the corresponding M. tuberculosis nucleotide sequence. Significant homology with many other 70kD heat shock proteins from a variety of prokaryotes and eukaryotes was also found. However, the M. leprae nucleotide sequence was not available in GENBANK69 for comparison. Using the alignment obtained for M. paratuberculosis and M. tuberculosis , two primers were selected for use in PCR amplification. Primer PAS77 (5'-CCGTCGGTGCAGATCCAGGT-3'; SEQ ID NO:14) was derived from the sense strand of the M. paratuberculosis sequence from nucleotides 1415-1434. Primer PAS78 (5'-GAACTTCTCCGTCTGGTAGA-3'; SEQ ID NO:15) was derived from the antisense strand of the M. paratuberculosis sequence from nucleotides 1763-1744. These primers were used in a PCR amplification reaction using several mycobacterial and non-mycobacterial DNAs as templates. PCR primers were synthesized on an Applied Biosystems 380B Synthesizer as recommended by the manufacturer, deprotected at 50°C and purified through an Oligonucleotide Purification Cartridge (Applied Biosystems, Inc.). PCR was performed in 25-100µl reaction volumes consisting of 10mM Tris-HCl pH 8.3, 50mM KCl, 1.5mM MgCl 2 , .001% (w/v) gelatin, 200µM dATP, 200µM dCTP, 200 µM dGTP, 200µM TTP, 1.0µM of each primer, 100ng/100µl of genomic DNA as template or 50ng/100µl plasmid DNA as template. The reactions were overlaid with mineral oil and heated to 95°C for 5 min. 2.5 Units/100µl of AMPLITAQ polymerase (Perkin Elmer Cetus, Nonwalk, CT) were added and the cycling was started. The samples were typically incubated at 94°C for 1 min. 30 sec., 37-50°C for 2 min., 72°C for 3 min. for 25-30 cycles. This was followed by a 7 min. incubation at 72°C and storage at 4°C. There was a distinct 349 bp PCR product in all of the Mycobacteria tested, including M. africanum, M. avium, M. bovis M. bovis-BCG, M. chelonae, M. fortuitum, M. gordonae, M. intracellulare, M. kansasii, M. scrofulaceum and M. tuberculosis . The primers showed no cross-reactivity to E. coli, N. asteroides and R. rhodochrous. As smaller internal oligonucleotides based on this sequence are required for nucleic acid amplification, as in SDA, it had to be determined whether there were highly conserved regions within this 349 bp product. The 349 bp amplification product (corresponding to nucleotides 1415-1763 of M. paratuberculosis ) was subcloned and sequenced from eleven different Mycobacteria, which included M. africanum, M. avium, M. bovis, M. bovis-BCG, M. chelonae, M. fortuitum, M. gordonae, M. intracellulare, M. kansasii, M. scrofulaceum, and M. tuberculosis. Sequencing was done using the Applied Biosystems 373A DNA sequencer using the Taq Dye Primer Cycle Sequencing Kit as recommended by the manufacturer. The sequences of the amplification products corresponding to nucleotides 1415-1763 of M. paratuberculosis are identified herein as SEQ ID NO: 1 through SEQ ID NO: 11. These sequences were aligned to design probes for genus specific detection of Mycobacteria by nucleic acid amplification and hybridization. RHODOCOCCUS RHODOCHROUS ANALOGOUS 70K ANTIGEN SEQUENCE To determine whether an analogous sequence existed in Rhodococcus rhodochrous, an R. rhodochrous λ-zap II library was constructed. R. rhodochrous genomic DNA was partially digested with Sau 3 AI and fragments between 0.5 and 8 kb were pooled. The fragments were then partially filled in using dGTP and dATP. The λ-zap II vector was prepared by digestion with Xho I followed by a partial fill-in using dCTP and dTTP. The R. rhodochrous and λ-zap II were then ligated together to form the library (CloneTech). The number of independent clones was 1.3 X 10 6 . The library was then amplified and screened for the presence of an analogous gene encoding the 70K antigen. The library was screened with the 349 bp PCR product from M. tuberculosis, M. avium, M. chelonae and M. gordonae. Two clones were obtained which contain overlapping sequence within the 349 bp region as well as upstream and downstream sequences. The selecte d R. rhodochrous sequence (SEQ ID NO:12) was aligned with the mycobacterial sequences to design probes for hybridization to and amplification of mycobacterial nucleic acids which would not cross react with R. rhodochrous. NOCARDIA ASTEROIDES ANALOGOUS 70K SEQUENCE To determine whether an analogous sequence existed in Nocardia asteroides, amplification and screening were performed essentially as described for the mycobacteria. A small internal section of the 349 bp region of the 70K hsp was identified in N. asteroides, subcloned and sequenced. Using this sequence information an oligonucleotide having the sequence of SEQ ID NO:26 was designed. This oligonucleotide corresponds to the antisense strand of the M. paratuberculosis sequence from nucleotide 1604-1585 with the addition of an Eco R1 site near the 5' end. The 3' end of SEQ ID NO:26 is complementary to mycobacteria target sequences and is designated the "primer binding site" in the Sequence Listing. It will be understood that the mycobacteria-complementary segment (i.e., the "primer binding site") of SEQ ID NO:26 may also be used alone as a probe in applications other than SDA. As will be described below, other probes of the invention have similar structures, i.e., a mycobacteria-complementary sequence at the 3' end with a Hin cII site immediately 5' to it and some additional 5' sequence to facilitate SDA. For each of these probes, the complementary segment is listed as a "primer binding site" in the Sequence Listing to indicate its complementary to mycobacterial nucleic acid sequences. It should be understood for all these probes that for identification and detection applications other than SDA the complementary primer binding site may be used alone (with or without appropriate labels) to obtain genus-specific hybridization to mycobacterial nucleic acid (e.g., as PCR primers or labeled hybridization probes). To design an oligonucleotide upstream (5') to the region of SEQ ID NO:26, the homologies of the 70K proteins of M. paratuberculosis and M. leprae were analyzed. Based on several conserved regions (Gupta, et al.), degenerate oligonucleotides were designed. SEQ ID NO:25 is degenerate in the third position of four codons and degenerate in the second and third positions of one codon. At its 3' end SEQ ID NO:25 corresponds to the sense strand of the M. paratuberculosis sequence from nucleotide 1211-1230 with the addition of an Eco R1 site near the 5' end. SEQ ID NO:26 corresponds to nucleotides 1585-1604 of M. paratuberculosis. A product 393 bp in length was amplified from N. asteroides by PCR using these two oligonucleotides. This product was subcloned into the Eco R1 site of pUC18 (Pharmacia). The clones were then sequenced on an Applied Biosystems 373A DNA sequencer using the Taq Dye Primer Cycle Sequencing Kit as recommended by the manufacturer. To obtain the downstream (3') Portion of the 349 bp region, oligonucleotides SEQ ID NO:27 and SEQ ID NO:28 were used in a PCR amplification reaction. SEQ ID NO:27 is the complementary oligonucleotide to SEQ ID NO:26 but does not contain an Eco R1 site at the 5' end. SEQ ID NO:28 was designed using the DNA sequence alignment of M. paratuberculosis and R. rhodochrous and corresponds to the antisense strand of the M. paratuberculosis sequence from nucleotide 1910-1927. This amplification therefore produced a product which slightly overlapped the sequence of the 393 bp amplification product at its 5' end and extended downstream a total of 342 bp. The 342 bp segment was subcloned into the Sma I site of pUC18. The clones were sequenced as before. The sequences of the 393 and 342 bp amplification products of N. asteroides were overlapped and analyzed to obtain the portion of the sequence corresponding to the 349 bp segment of M. paratuberculosis (SEQ ID NO:13). SEQ ID NO:13 was aligned with the mycobacterial sequences to select non-cross reacting sequences. ADDITIONAL UPSTREAM SEQUENCES FROM FOUR MYCOBACTERIA SPECIES The same degenerate PCR primers used to obtain the analogous N. asteroides sequence described above (primers SEQ ID NO:25 and SEQ ID NO:26) were used to amplify a 204 bp product from M. avium, M. gordonae, M. kansasii and M. tuberculosis. This product was subcloned into the Eco R1 site of pUC18 (Pharmacia). The clones were sequences on an Applied Biosystems 373A sequencer using the Taq Dye Primer Cycle Sequencing Kit as recommended by the manufacturer. These sequences were aligned with each other, the previously obtained N. asteroides (393 bp segment) and R. rhodochrous sequences, and the published M. paratuberculosis sequence to design probes for genus-specific detection of Mycobacteria by nucleic acid amplification and hybridization. The sequences from these species correspond to nucleotides 1211-1414 of M. paratuberculosis, with the exception of the R. rhodochrous sequence which correponds to nucleotides 1265-1414. They are listed in SEQ ID NO:29, SEQ ID NO:30, SEQ ID NO:31, SEQ ID NO:32, SEQ ID NO:33 and SEQ ID NO:34. SDA OF THE GENE ENCODING THE 70K ANTIGEN Oligonucleotides were synthesized on an Applied Biosystems 380B Synthesizer using β cyanoethyl phosphoramidite chemistry as recommended by the manufacturer. The oligonucleotides were deprotected at 50°C and gel purified as previously described (Ausubel, et al.) Strand displacement amplification reactions were performed essentially as described by Walker, et al., Nuc. Acids Res. (1992), supra , in a 10-50 ml volume consisting of 6mM MgCl 2 , 1mM each dGTP, dCTP, TTP and α-thio dATP, 100µg/ml acelated bovine serum albumin, 50mM KPO 4 pH 7.6, 3% (v/v) aqueous N-methyl-pyrrolidinone (NMP), 0.5µM primers S 1 and S 2 , 0.05µM primers B1 and B2, 3 units/µl Hin cII, 0.1 unit/µl exo - Klenow DNA polymerase (United States Biochemical) (Derbyshire, et al. (1988) Science 240 :100-201) and varying amounts of target DNA. In some instances SDA reactions were performed to generate dU-substituted product. In these reactions the MgCl 2 concentration was 7mM, 10% glycerol was used in lieu of NMP, and the nucleotides dUTP (0.5mM), dGTP, dCTP and α-thio dATP (0.2mM) were substituted. Prior to the addition of Hin cII and exo - Klenow, the reactions were heated at 95°C for 2 min. to denature the target DNA followed by 2 min. at 37-40°C to anneal the primers. Following the addition of the enzymes the reactions were incubated at 37-40°C for 2 hr. for amplification. Amplification was terminated by heating for 10 min. at 65°C. Product was detected by primer extension of a 32 -P labeled probe and analyzed by denaturing polyacrylamide gel electrophoresis as described previously (Walker, et al.). Probes designed by the above procedure which were directed to two regions of the 70K gene showed no cross reactivity with N. asteroides or R. rhodochrous and maintained genus specificity. These probes were tested as primers in SDA reactions to confirm genus-specificity. The first region was amplified with primer sets SEQ ID NO:20, SEQ ID NO:21, SEQ ID NO:22, SEQ ID NO:23 AND SEQ ID NO:24. SEQ ID NO:21, SEQ ID NO:22 and SEQ ID NO: 20 are S 1 and S 2 (amplification) primers and SEQ ID NO:23 and SEQ ID NO:24 are B 1 and B 2 (bumper) primers, as defined by Walker, et al, Nucleic Acids Res., supra. SEQ ID NO:20, SEQ ID NO:21 and SEQ ID NO:22 have complementary primer binding sites at their 3' ends and Hin cII sites immediately 5' to the complementary segment. This first region includes a three base pair mismatch with SEQ ID NO:20, and a one base pair mismatch with SEQ ID NO:21/SEQ ID NO:22 between R. rodochrous and N. asteroides respectively. Upon amplification, this region showed a sensitivity for M. avium at 10,000 molecules and no cross reactivity with N. asteroides er R. rhodochrous . These genus-specific probes may also be used for genus-specific detection of mycobacterial nucleic acid by hybridization as described above. A separate region of the 70K hsp was amplified employing the probe sets SEQ ID NO:16, SEQ ID NO:17, SEQ ID NO:18 and SEQ ID NO:19, where SEQ ID NO:17 and SEQ ID NO:18 were used as S 1 and S 2 primers and SEQ ID NO:16 and SEQ ID NO:19 were used as B 1 and B 2 primers. SEQ ID NO:17 and SEQ ID NO:18 are complementary to mycobacterial sequences at their 3' ends, as shown in the Sequence Listing, and have Hin cII sites immediately upstream of the primer binding site. The 5' ends contain additional sequences which facilitate amplification by SDA. The region defined by these probe sets amplified all mycobacterial species tested, which included M. tuberculosis, M .fortuitum, M. chelonae, M. gordonae, M. avium, M. intracelluiare, M. bovis, M. kansasii, M. africanum, and M. scrofulaceum. There was no amplification in the non-mycobacterial species tested, which included N. asteroides, R. rhodochrous, Bordetella pertussis, Candida albicans, Corynebacterium diphtheriae, Escherichia coli, Flavobacterium maningisepticum, Streptococcus pneumoniae, Acinetobacter lwoffi, Enterobacter aerogenes, Enterobacter cloacae, Haemophilus influenzae type b, Klebsiella pneumoniae, Listeria monocytogenes, Moraxella osloensis, Morganella morganii, Neisseria lactamica, Neisseria meningitidis, Oerskovia turbata, Proteus vulgaris, Pseudomonas aeruginosa, Serratia marcescens. Shigella dysenteriae, Staphylococcus aureus, Staphylococcus epidermidis and Streptococcus pyogenes. The approximate sensitivity of this system is about 1,000 to 10,000 molecules of mycobacterium genomic DNA. The probes as well may be used in hybridization reactions for genus-specific detection of mycobacterial nucleic acids. Based on the homology of the sequence alignments from nucleotides 1211-1414 of M. avium, M. gordonae, M. kansasii, M. tuberculosis and M. paratuberculosis, a conserved region was chosen for SDA amplification. Also, by aligning the previously obtained N. asteroides and R. rhodochrous sequences, primers were designed to take advantage of mismatches to eliminate cross-reactivity. The S 1 primer (SEQ ID NO:35) has a 3' ultimate mismatch in addition to an internal mismatch in N. asteroides and R. rhodochrous . The S 2 primer (SEQ ID NO:36) has a three base pair mismatch on the 3' end in N. asteroides and R. rhodochrous. Both SEQ ID NO:35 and SEQ ID NO:36 have complementary primer binding sequences at the 3' end, Hin cII sites, and additional 5' sequences as previously described for certain of the other probes. Both primers are identical in the five mycobacteria species. B 1 and B 2 primers used were SEQ ID NO:37 and SEQ ID NO:19. SDA amplification reactions were performed as described previously. The approximate sensitivity of this amplification system is 2,000 molecules of M. tuberculosis DNA.

Claims: An oligonucleotide having a sequence selected from the group consisting of SEQ ID NO:16, SEQ ID NO:17, SEQ ID NO:18, SEQ ID NO:19, SEQ ID NO:20, SEQ ID NO:21, SEQ ID NO:22, SEQ ID NO:23, SEQ ID NO:24, SEQ ID NO:35, SEQ ID NO:36 and SEQ ID NO:37. A nucleotide having a sequence selected from the group consisting of SEQ ID NO: 1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:29, SEQ ID NO:30, SEQ ID NO:31, SEQ ID NO:32 and sequences complementary thereto. An oligonucleotide having a sequence selected from the group consisting of SEQ ID NO:14 and SEQ ID NO:15. A method for genus-specific amplification of mycobacterial nucleic acid comprising the steps of. a) hybridizing to the mycobacterial nucleic acid at least two oligonucleotides selected from the group consisting of SEQ ID NO:20, SEQ ID NO:21, SEQ ID NO:22, SEQ ID NO:23 and SEQ ID NO:24, and; b) amplifying a genus-specific segment of the mycobacterial nucleic acid defined by the hybridized probes to produce a genus-specific amplification product. A method for genus-specific amplification of mycobacterial nucleic acid comprising the steps of: a) hybridizing to the mycobacterial nucleic acid at least two oligonucleotides selected from the group consisting of SEQ ID NO:16, SEQ ID NO:17, SEQ ID NO:18 and SEQ ID NO:19, and; b) amplifying a genus-specific segment of the mycobacterial nucleic acid defined by the hybridized probes to produce a genus-specific amplification product. A method for genus-specific amplification of mycobacterial nucleic acid comprising the steps of: a) hybridizing to the mycobacterial nucleic acid at least two oligonucleotides selected from the group consisting of SEQ ID NO:35, SEQ ID NO:36, SEQ ID NO:37 and SEQ ID NO:19, and; b) amplifying a genus-specific segment of the mycobacterial nucleic acid defined by the hybridized probes to produce a genus-specific amplification product. The method according to any one of Claims 5, 6, or 7 further comprising detecting the genus-specific amplification product. The method according to any one of Claims 5, 6 or 7 wherein the mycobacterial nucleic acid is amplified by strand displacement amplification. A method for genus-specific detection of mycobacterial nucleic acid comprising the steps of: a) hybridizing to the mycobacterial nucleic acid at least one probe selected from the group consisting of SEQ ID NO:16, SEQ ID NO:17, SEQ ID NO:18, SEQ ID NO:19, SEQ ID NO:20, SEQ ID NO:21, SEQ ID NO:22, SEQ ID NO:23, SEQ ID NO:24, SEQ ID NO:35, SEQ ID NO:36 and SEQ ID NO:37, and; b) detecting the hybridized probe.

Inventors: LITTLE MICHAEL C, SHANK DARYL D, SPEARS PATRICIA A, LITTLE, MICHAEL C., SHANK, DARYL D., SPEARS, PATRICIA A.
Applicants: BECTON DICKINSON CO, BECTON, DICKINSON AND COMPANY
Application year: 1994
Main classification: C12Q1
IPC codes: C12Q1, C12N15, C07H21